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This is the user manual for Biblio-MetReS. This manual will help you to understand all the functionalities of the applications and help you use the application appropriately.

Biblio-MetReS is an application whose goal is to mine published scientific documents in order to reconstruct protein and gene co-occurrence networks. These networks form the basis of an initial network reconstruction that will allow you to understand what does your protein or gene of interest do in your favorite organisms and with which other proteins or genes does your protein work in order to achieve its appropriate biological function. Biblio-MetReS relies on a central database with the genomes and gene annotation of more than 1000 organisms. It is this repository of gene names and functions that is accessed by the application when you choose your organism of interest.

Biblio-MetReS is conceived to be used by Molecular and Cellular Biologists. It is user-friendly. It can mine information from literature that is available online. Its analysis can be restricted to abstracts of scientific papers or to the full documents, depending on your choice of options.

This manual will explain how these options work and which ones you should use, depending on what your goal is.

A couple of warnings are at hand. First, this is the first stable version of Biblio-MetReS. We have tested extensively and it ran appropriately in our hands. However, we do not guarantee that the results are error-free and you use it at your own responsibility. Second, given that Biblio-MetReS searches the Internet and analyzes documents on the fly, you search and analysis might take a while. It may not look like it, but a very large amount of information is being analyzed as you run the program. As more people use Biblio-MetReS, the process of search-analysis will become faster, because results from previous iterations of any given search-analysis will be stored locally and the program will only need to analyze new documents that are published since the last time a specific search was executed. Third, you need to have an active Internet connection to use Biblio-MetReS. The application checks our local server to download gene information and previously compiled searches and uses the Internet to search for and download new documents.